CBIcall
Configuration-driven framework for reproducible cohort-scale variant calling
CBIcall (CNAG Biomedical Informatics framework for variant calling) is a configuration-driven framework for reproducible variant calling in large sequencing cohorts.
CBIcall validates a parameters YAML file against approved workflow and resource contracts, creates a deterministic run directory, and records structured reports for audit and run comparison.
Execution Contract
CBIcall separates routine user input from framework-managed implementation and resource definitions.
| Contract layer | Purpose |
|---|---|
| Parameters YAML | User analysis intent: inputs, pipeline, mode, genome, backend, and runtime options. |
| Workflow registry | Approved workflow implementations and backend-specific entrypoints. |
| Resource catalog | External references, tool/resource bundles, compatibility rules, and resource identity. |
This separation is the basis for validation, provenance capture, and repeatable run comparison across computing environments.
What CBIcall Does
CBIcall does not re-implement alignment or variant-calling algorithms; those steps remain in curated pipeline implementations built from established tools such as BWA, GATK, MToolBox, Snakemake, Nextflow, Cromwell, and selected nf-core pipelines.
- validates the parameters YAML and compatibility contract before launch
- resolves Bash, Snakemake, Nextflow, or Cromwell workflow backends
- checks the selected workflow against the resource catalog when resources are required
- records logs, run reports, workflow fingerprints, resource identity, output inventories, normalized VCF hashes, and run comparisons when available
Pipelines and Backends
CBIcall separates the analysis pipeline from the workflow backend that executes it.
| Layer | Current scope |
|---|---|
| Out-of-box analysis pipelines | WES, WGS, and mtDNA variant calling |
| Workflow backends | Bash, Snakemake, Nextflow, and Cromwell |
| External provider entries | Registered nf-core pipelines launched through the Nextflow backend |
The bundled cbicall-core WES/WGS/mtDNA workflows use the CBIcall resource
bundle. Registered nf-core entries can be validated and launched without that
bundle; Nextflow/nf-core manages the external pipeline's own test data,
containers, and references.
Use Included Pipelines for the shipped analyses and Native Backends for the supported workflow backends.
Installation at a Glance
| Use case | Method |
|---|---|
| Local workstation or server | PyPI, Docker, or a source checkout for development |
| HPC cluster | PyPI, Apptainer / Singularity, or site modules |
| Cloud reproducibility check | Google Cloud |
| Development or debugging | Non-containerized source install |
Where to Go Next
| Goal | Page |
|---|---|
| Try nf-core without the CBIcall bundle | Quickstart |
| Run the native shipped test data | Quickstart |
| Run WES/WGS data | WES Example |
| Run mtDNA analysis | mtDNA Example |
| See included pipelines | Included Pipelines |
| Understand workflow backends | Native Backends |
| Understand output files | Outputs |
| See the system design | Architecture |